☰ Navigation Tabs
Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with compound 7d, co-crystallized
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4V2Y
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 294 15 % PEG 6K, 5 % Glycerol
Crystal Properties Matthews coefficient Solvent content 1.79 31.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 31.643 α = 90 b = 52.482 β = 95.79 c = 59.242 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M-F 2017-05-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 1 SLS X10SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) CC (Half) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.1 39.2 99.1 0.053 1 17.67 6.3 77977
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.1 1.16 95.1 0.4 0.92 3.64 5.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4v2y 1.1 39.2 74053 3898 99 0.12348 0.12211 0.1243 0.14963 0.1487 RANDOM 17.049
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] 0.15 1.7 -0.23 -0.26
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 46.684 r_dihedral_angle_2_deg 31.055 r_sphericity_bonded 21.719 r_scangle_other 18.744 r_scbond_it 16.057 r_scbond_other 16.049 r_dihedral_angle_4_deg 14.431 r_long_range_B_refined 12.742 r_dihedral_angle_3_deg 11.32 r_long_range_B_other 11.26
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 46.684 r_dihedral_angle_2_deg 31.055 r_sphericity_bonded 21.719 r_scangle_other 18.744 r_scbond_it 16.057 r_scbond_other 16.049 r_dihedral_angle_4_deg 14.431 r_long_range_B_refined 12.742 r_dihedral_angle_3_deg 11.32 r_long_range_B_other 11.26 r_rigid_bond_restr 8.179 r_dihedral_angle_1_deg 6.23 r_angle_refined_deg 2.449 r_angle_other_deg 1.973 r_mcangle_it 1.89 r_mcangle_other 1.889 r_mcbond_it 1.771 r_mcbond_other 1.77 r_chiral_restr 0.455 r_bond_refined_d 0.031 r_gen_planes_refined 0.016 r_bond_other_d 0.015 r_gen_planes_other 0.015 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1663 Nucleic Acid Atoms Solvent Atoms 276 Heterogen Atoms 38
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MOLREP phasing